This script uses the data.frame “data”, loaded from s01.RData. That is, all rows with C==“C” has been excluded for exploratory data analysis.
# ------------------------------------------------------------------
# Prepare environment
# ------------------------------------------------------------------
# load packages
source(file=file.path("Scripts","Setup","setup01_projectPackages.R"))
# load output from s01_DatasetPrep.R
load(file=file.path("Scripts","s01.RData"))
# White background in plots
theme_set(theme_bw()) # to be replaced with a azTheme
update_geom_defaults("point", list(shape = 1))
Are the plots and tables also being written to file?
## [1] TRUE
The total number of observations in the dataset (with/without BLQ data) and the %BLQ.
## [1] 1491
## [1] 1255
## [1] 15.83
Number of samples and occasions/subject (with/without BLQ)
## nDV nOcc maxTAFD
## Min. :23.00 Min. :2 Min. :215.8
## 1st Qu.:25.00 1st Qu.:2 1st Qu.:215.8
## Median :25.00 Median :2 Median :215.8
## Mean :24.85 Mean :2 Mean :215.8
## 3rd Qu.:25.00 3rd Qu.:2 3rd Qu.:215.8
## Max. :25.00 Max. :2 Max. :215.8
## nDV nOcc maxTAFD
## Min. :14.00 Min. :2 Min. :196.0
## 1st Qu.:16.00 1st Qu.:2 1st Qu.:198.0
## Median :23.00 Median :2 Median :215.8
## Mean :20.92 Mean :2 Mean :208.8
## 3rd Qu.:25.00 3rd Qu.:2 3rd Qu.:215.8
## Max. :25.00 Max. :2 Max. :215.8
Number of individuals and samples per dose group
| Dose | nSubjects | nConc | percentBlqByDose |
|---|---|---|---|
| 100 | 15 | 373 (25) | 18.5 |
| 150 | 15 | 371 (24.9) | 8.09 |
| 25 | 15 | 373 (25) | 33.8 |
| 300 | 15 | 374 (25.1) | 2.94 |
Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited as LLOQ/2.
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Right: un-transformed scale. Left: log-transformed y-axis. Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited as LLOQ/2.
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Right: un-transformed scale. Left: log-transformed y-axis. Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited as LLOQ/2.
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Right: un-transformed scale. Left: log-transformed y-axis. Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited at LLOQ/2.
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Right: un-transformed scale. Left: log-transformed y-axis. Lines connect data from one occasion within a subject. Colour indicate subject. Points indicate measured data. Dashed blue line show the lower limit of quantification. BLQ data is prited at LLOQ/2.
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The section below generates a list of individual plots with different combinations of the following settings:
Concentration versus time after first dose or time after dose
Log scale and untransformed scale
Free/fixed scales for axes across individuals
Not all plots are going to be useful, you can just comment out/delete the ones you do not want to keep.
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